(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT)
`
`(19) World Intellectual Property Organization
`International Bureau
`
`(43) International Publication Date
`16 September 2010 (16.09.2010)
`
`PCT
`
`1111111111111111 IIIIII IIIII 111111111111111 II Ill lllll lllll 11111111111111111111111111111111111111
`
`(10) International Publication Number
`WO 2010/105243 Al
`
`(51) International Patent Classification:
`C12Q 1/32 (2006.01)
`A61P 35/00 (2006.01)
`
`(21) International Application Number:
`PCT/US20I0/027253
`
`(22) International Filing Date:
`
`(25) Filing Language:
`
`(26) Publication Language:
`
`12 March 2010 (12.03.2010)
`
`English
`
`English
`
`(8l)
`
`Seymour Street, Concord, MA Ol 742 (US). SU, Shinsan
`[US/US]; 346 Hartman Road, Newton, MA 02459 (US).
`YEN, Katharine [US/US]; 6 Shirley Road, Wellestey,
`MA 02482 (US).
`
`(74) Agent: MCCARTY, Catherine, M.; Lando & Anastasi,
`Lip, One Main Street, Eleventh Floor, Cambridge, MA
`02142 (US).
`
`Designated States (unless otherwise indicated, for every
`kind of national protection available): AE, AG, AL, AM,
`AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ,
`CA,CH,CL,CN,CO,CR,CU,CZ,DE,DK,DM,DO,
`DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT,
`HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP,
`KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD,
`ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI,
`NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD,
`SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR,
`TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
`
`(30) Priority Data:
`61/160,253
`61/160,664
`61/173,518
`61/180,609
`61/220,543
`61/227,649
`61/229,689
`61/253,820
`61/266,929
`
`13 March 2009 (13.03.2009)
`16 March 2009 (16.03.2009)
`28 April 2009 (28.04.2009)
`22 May 2009 (22.05.2009)
`25 June 2009 (25.06.2009)
`22 July 2009 (22.07.2009)
`29 July 2009 (29.07.2009)
`21 October 2009 (21.l0.2009)
`4 December 2009 (04.12.2009)
`
`us
`us
`us
`us
`us
`us
`us
`us
`us
`(71) Applicant (for all designated States except US): AGIOS
`PHARMACEUTICALS, INC. [US/US]; 38 Sidney
`Street, Cambridge, MA 02139 (US).
`
`(72)
`(75)
`
`;;;;;;;;;;;;;;
`;;;;;;;;;;;;;;
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`;;;;;;;;;;;;;; ---;;;;;;;;;;;;;; -;;;;;;;;;;;;;;
`;;;;;;;;;;;;;; -
`
`Inventors; and
`Inventors/Applicants (for US only): DANG, Lenny [US/
`US]; 30 Union Street, #201, Boston, MA 02118 (US).
`FANTIN, Valeria [AR/US]; 195 Binney Street, Apt
`4515, Cambridge, MA 02142 (US). GROSS, Stefan [US/
`US]; 14 Park Street #I, Brookline, MA 02446 (US).
`JANG, Hyun Gyung [KR/US]; 6 William Street, Arling(cid:173)
`ton, MA 02476 (US). JIN, Shengfang [US/US]; 6
`Audubon Drive, Newton, MA 02467 (US). SALITURO,
`Frank [US/US]; 25 Baker Drive, Marlborough, MA
`01752 (US). SAUNDERS, Jeffrey, O. [US/US]; 117
`
`(84) Designated States (unless otherwise indicated, for every
`kind of regional protection available): ARIPO (BW, GH,
`GM, KE, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, ZM,
`ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ,
`TM), European (AT, BE, BG, CH, CY, CZ, DE, DK, EE,
`ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV,
`MC, MK, MT, NL, NO, PL, PT, RO, SE, SI, SK, SM,
`TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW,
`ML, MR, NE, SN, TD, TG).
`
`Published:
`
`with international search report (Art. 21 (3))
`
`before the expiration of the time limit for amending the
`claims and to be republished in the event of receipt of
`amendments (Rule 48.2(h))
`
`-;
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`;;;;;;;;;;;;;;
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`~ "" M "' 0
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`0
`,-.-1
`0
`M
`0 (54) Title: METHODS AND COMPOSITIONS FOR CELL-PROLIFERATION-RELATED DISORDERS
`~ (57) Abstract: Methods of treating and evaluating subjects having neoactive mutants are described herein.
`
`Rigel Exhibit 1009
`Page 1 of 245
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`WO 2010/105243
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`PCT/0S2010/027253
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`METHODS AND COMPOSITIONS FOR CELL-PROLIFERATION(cid:173)
`RELATED DISORDERS
`
`CLAIM OF PRIORITY
`This application claims priority to U.S.S.N. 61/160253, filed March 13, 2009;
`U.S.S.N. 61/160664, filed March 16, 2009; U.S.S.N. 61/173518, filed April 28, 2009;
`U.S.S.N. 61/180609, filed May 22, 2009; U.S.S.N. 61/220543, filed June 25, 2009;
`U.S.S.N. 61/227649, filed July 22, 2009; U.S.S.N. 61/229689, filed July 29, 2009;
`U.S.S.N. 61/253820, filed October 21, 2009; and U.S.S.N. 61/266929, filed
`December 4, 2009, the contents of each of which are incorporated herein by reference.
`
`FIELD OF THE INVENTION
`The invention relates to methods and compositions for evaluating and treating
`cell proliferation-related disorders, e.g., proliferative disorders such as cancer.
`
`BACKGROUND
`Isocitrate dehydrogenase, also known as IDH, is an enzyme which participates
`in the citric acid cycle. It catalyzes the third step of the cycle: the oxidative
`decarboxylation of isocitrate, producing alpha-ketoglutarate ( a-ketoglutarate or a-KG)
`and CO2 while converting NAD+ to NADH. This is a two-step process, which
`involves oxidation of isocitrate (a secondary alcohol) to oxalosuccinate (a ketone),
`followed by the decarboxylation of the carboxyl group beta to the ketone, forming
`alpha-ketoglutarate. Another isoform of the enzyme catalyzes the same reaction;
`however this reaction is unrelated to the citric acid cycle, is carried out in the cytosol
`as well as the mitochondrion and peroxisome, and uses NADP+ as a cofactor instead
`ofNAD+.
`
`SUMMARY OF THE INVENTION
`Methods and compositions disclosed herein relate to the role played in disease
`by neoactive products produced by neoactive mutant enzymes, e.g., mutant metabolic
`pathway enzymes. The inventors have discovered, inter alia, a neoactivity associated
`with IDH mutants and that the product of the neoactivity can be significantly elevated
`in cancer cells. Disclosed herein are methods and compositions for treating, and
`methods of evaluating, subjects having or at risk for a disorder, e.g., a cell
`
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`proliferation-related disorder characterized by a neoactivity in a metabolic pathway
`enzyme, e.g., IDH neoactivity. Such disorders include e.g., proliferative disorders
`such as cancer. The inventors have discovered and disclosed herein novel therapeutic
`agents for the treatment of disorders, e.g., cancers, characterized by, e.g., by a
`neoactivity, neoactive protein, neoactive mRNA, or neoactive mutations. In
`embodiments a therapeutic agent reduces levels of neoactivity or neoactive product or
`ameliorates an effect ofa neoactive product. Methods described herein also allow the
`identification of a subject, or identification of a treatment for the subject, on the basis
`of neaoctivity genotype or phenotype. This evaluation can allow for optimal
`matching of subject with treatment, e.g., where the selection of subject, treatment, or
`both, is based on an analysis of neoactivity genotype or phenotype. E.g., methods
`describe herein can allow selection of a treatment regimen comprising administration
`of a novel compound, e.g., a novel compound disclosed herein, or a known compound,
`e.g., a known compound not previously recommended for a selected disorder. In
`embodiments the known compound reduces levels of neoactivity or neoactive product
`or ameliorates an effect of a neoactive product. Methods described herein can guide
`and provide a basis for selection and administration of a novel compound or a known
`compound, or combination of compounds, not previously recommended for subjects
`having a disorder characterized by a somatic neoactive mutation in a metabolic
`pathway enzyme. In embodiments the neoactive genotype or phenotype can act as a
`biomarker the presence of which indicates that a compound, either novel, or
`previously known, should be administered, to treat a disorder characterized by a
`somatic neoactive mutation in a metabolic pathway enzyme. Neoactive mutants of
`IDHl having a neoactivity that results in the production of 2-hydroxyglutarate, e.g.,
`R-2-hydroxyglutarate and associated disorders are discussed in detail herein. They
`are exemplary, but not limiting, examples of embodiments of the invention.
`While not wishing to be bound by theory it is believed that the balance
`between the production and elimination of neoactive product, e.g., 2HG, e.g., R-2HG,
`is important in disease. N eoactive mutants, to varying degrees for varying mutations,
`increase the level of neoactive product, while other processes, e.g., in the case of 2HG,
`e.g., R-2HG, enzymatic degradation of 2HG, e.g., by 2HG dehydrogenase, reduce the
`level of neoative product. An incorrect balance is associated with disease. In
`embodiments, the net result of a neoactive mutation at IDHl or IDH2 result in
`increased levels, in affected cells, of neoactive product, 2HG, e.g., R-2HG,
`
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`Accordingly, in one aspect, the invention features, a method of treating a
`subject having a cell proliferation-related disorder, e.g., a disorder characterized by
`unwanted cell proliferation, e.g., cancer, or a precancerous disorder. The cell
`proliferation-related disorder is characterized by a somatic mutation in a metabolic
`pathway enzyme. The mutation is associated with a neoactivity that results in the
`production of a neoactivity product. The method comprises: administering to the
`subject a therapeutically effective amount of a therapeutic agent described herein, e.g.,
`a therapeutic agent that decreases the level of neoactivity product encoded by a
`selected or mutant somatic allele, e.g., an inhibitor of a neoactivity of the metabolic
`pathway enzyme (the neoactive enzyme), a therapeutic agent that ameliorates an
`unwanted affect of the neoactivity product, or a nucleic acid based inhibitor, e.g., a
`dRNA which targets the neoactive enzyme mRNA,
`to thereby treat the subject.
`In an embodiment the subject is a subject not having, or not diagnosed as
`having, 2-hydroxyglutaric aciduria.
`In an embodiment the subject has a cell proliferation-related disorder, e.g., a
`cancer, characterized by the neoactivity of the metabolic pathway enzyme encoded by
`selected or mutant allele.
`In an embodiment the subject has a cell proliferation-related disorder, e.g., a
`cancer, characterized by the product formed by the neoactivity of the metabolic
`pathway enzyme encoded by selected or mutant allele.
`In one embodiment, the metabolic pathway is selected from a metabolic
`pathway leading to fatty acid biosynthesis, glycolysis, glutaminolysis, the pentose
`phosphate shunt, nucleotide biosynthetic pathways, or the fatty acid biosynthetic
`pathway.
`In an embodiment the therapeutic agent is a therapeutic agent described herein.
`In an embodiment the method comprises selecting a subject on the basis of
`having a cancer characterized by the selected or mutant allele, the neoactivity, or an
`elevated level of neaoctivity product.
`In an embodiment the method comprises selecting a subject on the basis of
`having a cancer characterized by the product formed by the neoactivity of the protein
`encoded by selected or mutant allele, e.g., by the imaging and/or spectroscopic
`analysis, e.g., magnetic resonance-based analysis, e.g., MRI (magnetic resonance
`imaging) and/or MRS (magnetic resonance spectroscopy), to determine the presence,
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`distribution or level of the product of the neoactivity, e.g., in the case of an IDHI
`allele described herein, 2-hydroxyglutarate (sometimes referred to herein as 2HG),
`e.g., R-2-hydroxyglutarate (sometimes referred to herein as R-2HG).
`In an embodiment the method comprises confirming or determining, e.g., by
`direct examination or evaluation of the subject, or sample e.g., tissue, product (e.g.,
`feces, sweat, semen, exhalation, hair or nails), or bodily fluid (e.g., blood (e.g., blood
`plasma), urine, lymph, or cerebrospinal fluid or other sample sourced disclosed herein)
`therefrom, (e.g., by DNA sequencing, immuno analysis, or assay for enzymatic
`activity), or receiving such information about the subject, that the cancer is
`characterized by the selected or mutant allele.
`In an embodiment the method comprises confirming or determining, e.g., by
`direct examination or evaluation of the subject, the level of neoactivity or the level of
`the product of the neoactivity, or receiving such information about the subject. In an
`embodiment the presence, distribution or level of the product of the neoactivity, e.g.,
`in the case of an IDHI allele described herein, 2HG, e.g., R-2HG, is determined non(cid:173)
`invasively, e.g., by imaging methods, e.g., by magnetic resonance-based methods.
`In an embodiment the method comprises administering a second anti-cancer
`agent or therapy to the subject, e.g., surgical removal or administration of a
`chemotherapeutic.
`In another aspect, the invention features, a method of treating a subject having
`a cell proliferation-related disorder, e.g., a precancerous disorder, or cancer. In an
`embodiment the subject does not have, or has not been diagnosed as having, 2-
`hydroxyglutaric aciduria. The cell proliferation-related disorder is characterized by a
`somatic allele, e.g., a preselected allele, or mutant allele, of an IDH, e.g., IDHI or
`IDH2, which encodes a mutant IDH, e.g., IDHI or IDH2, enzyme having a
`neoactivity.
`
`In embodiments the neoactivity is alpha hydroxy neoactivity. As used herein,
`alpha hydroxy neoactivity refers to the ability to convert an alpha ketone to an alpha
`hydroxy. In embodiments alpha hydroxy neoactivity proceeds with a reductive
`cofactor, e.g., NADPH or NADH. In embodiments the alpha hydroxyl neoactivity is
`2HG neoactivity. 2HG neoactivity, as used herein, refers to the ability to convert
`alpha ketoglutarate to 2-hydroxyglutarate (sometimes referred to herein as 2HG), e.g.,
`R-2-hydroxyglutarate (sometimes referred to herein as R-2HG). In embodiments
`2HG neoactivity proceeds with a reductive cofactor, e.g., NADPH or NADH. In an
`
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`embodiment a neoactive enzyme, e.g., an alpha hydroxyl, e.g., a 2HG, neoactive
`enzyme, can act on more than one substrate, e.g., more than one alpha hydroxy
`substrate.
`
`The method comprises administering to the subject an effective amount of a
`therapeutic agent of type described herein to thereby treat the subject.
`In an embodiment the therapeutic agent: results in lowering the level of a
`neoactivity product, e.g., an alpha hydroxy neoactivity product, e.g., 2HG, e.g., R-
`2HG.
`
`In an embodiment the method comprises administering a therapeutic agent that
`lowers neoactivity, e.g., 2HG neoactivity. In an embodiment the method comprises
`administering an inhibitor of a mutant IDH protein, e.g., a mutant IDHl or mutant
`IDH2 protein, having a neoactivity, e.g., alpha hydroxy neoactivity, e.g., 2HG
`neoactivity.
`In an embodiment the therapeutic agent comprises a compound from Table
`24a or Table 24b or a compound having the structure of Formula (X) or (Formula (XI)
`described herein.
`In an embodiment the therapeutic agent comprises nucleic acid-based
`therapeutic agent, e.g., a dsRNA, e.g., a dsRNA described herein.
`In an embodiment the the therapeutic agent is an inhibitor, e.g., a polypeptide,
`peptide, or small molecule (e.g., a molecule ofless than 1,000 daltons), or aptomer,
`that binds to an IDHl mutant or wildtype subunit and inhibits neoactivity, e.g., by
`inhibiting formation of a dimer, e.g., a homodimer of mutant IDHl subunits or a
`heterodimer of a mutant and a wildype subunit. In an embodiment the inhibitor is a
`polypeptide. In an embodiment the polypeptide acts as a dominant negative with
`respect to the neoactivity of the mutant enzyme. The polypeptide can correspond to
`full length IDHl or a fragment thereof. The polypeptide need not be indentical with
`the corresponding residues of wildtype IDHl, but in embodiments has at least 60, 70,
`80, 90 or 95 % homology with wildtype IDHl.
`In an embodiment the therapeutic agent decreases the affinity of an IDH, e.g.,
`IDHl or IDH2 neoactive mutant protein for NADH, NADPH or a divalent metal ion,
`e.g., Mg2+ or Mn2+, or decreases the levels or availability of NADH, NADPH or
`divalent metal ion, e.g., Mg2+ or Mn2+, e.g., by competing for binding to the mutant
`enzyme. In an embodiment the enzyme is inhibited by replacing Mg2
`+ or Mn2
`+ with
`Ca2+.
`
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`In an embodiment the therapeutic agent is an inhibitor that reduces the level a
`neoactivity of an IDH, e.g., IDHI or IDH2, e.g., 2HG neoactivity.
`In an embodiment the therapeutic agent is an inhibitor that reduces the level of
`the product of a mutant having a neoactivity of an IDH, e.g., IDHl or IDH2 mutant,
`e.g., it reduces the level of2HG, e.g., R-2HG.
`In an embodiment the therapeutic agent is an inhibitor that:
`inhibits, e.g., specifically, a neoactivity of an IDH, e.g., IDHI or IDH2, e.g., a
`neoactivity described herein, e.g., 2HG neoactivity; or
`inhibits both the wildtype activity and a neoactivity of an IDH, e.g., IDHI
`orIDH2, e.g., a neoactivity described herein, e.g, 2HG neoactivity.
`In an embodiment the therapeutic agent is an inhibitor that is selected on the
`basis that it:
`inhibits, e.g., specifically, a neoactivity of an IDH, e.g., IDHl or IDH2, e.g., a
`neoactivity described herein e.g., 2HG neoactivity; or
`inhibits both the wildtype activity and a neoactivity of an IDHI, e.g., IDHl or
`IDH2, e.g., a neoactivity described herein, e.g., 2HG neoactivity.
`In an embodiment the therapeutic agent is an inhibitor that reduces the amount
`of a mutant IDH, e.g., IDHI or IDH2, protein or mRNA.
`In an embodiment the therapeutic agent is an inhibitor that interacts directly
`with, e.g., it binds to, the mutant IDH, e.g., IDHI or IDH2 mRNA.
`In an embodiment the therapeutic agent is an inhibitor that interacts directly
`with, e.g., it binds to, the mutant IDH, e.g., IDHl or IDH2, protein.
`In an embodiment the therapeutic agent is an inhibitor that reduces the amount
`of neoactive enzyme activity, e.g., by interacting with, e.g., binding to, mutant IDH,
`e.g., IDHl or IDH2, protein. In an embodiment the inhibitor is other than an antibody.
`In an embodiment the therapeutic agent is an inhibitor that is a small molecule
`and interacts with, e.g., binds, the mutant RNA, e.g., mutant IDHl or IDH2 mRNA
`(e.g., mutant IDHI mRNA).
`In an embodiment the therapeutic agent is an inhibitor that interacts directly
`with, e.g., binds, either the mutant IDH, e.g., IDHl or IDH2, protein or interacts
`directly with, e.g., binds, the mutant IDH mRNA, e.g., IDHl or IDH2 mRNA.
`In an embodiment the IDH is IDHI and the neoactivity is alpha hydroxy
`neoactivity, e.g., 2HG neoactivity. Mutations in IDHl associated with 2HG
`
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`neoactivity include mutations at residue 132, e.g., R132H, R132C, R132S, Rl32G,
`R132L, or Rl32V (e.g., R132H or Rl32C).
`In an embodiment the IDH is IDH2 and the neoactivity of the IDH2 mutant is
`alpha hydroxy neoactivity, e.g., 2HG neoactivity. Mutations in IDH2 associated with
`2HG neoactivity include mutations at residue 172, e.g., Rl 72K, Rl 72M, Rl 72S,
`Rl 72G, or Rl 72W.
`Treatment methods described herein can comprise evaluating a neoactivity
`genotype or phenotype. Methods of obtaining and analyzing samples, and the in vivo
`analysis in subjects, described elsewhere herein, e.g., in the section entitled, "Methods
`of evaluating samples and/or subjects," can be combined with this method.
`In an embodiment, prior to or after treatment, the method includes evaluating
`the growth, size, weight, invasiveness, stage or other phenotype of the cell
`proliferation-related disorder.
`In an embodiment, prior to or after treatment, the method includes evaluating
`the IDH, e.g., IDHl or IDH2, alpha hydroxyl neoactivity genotype, e.g., 2HG,
`genotype, or alpha hydroxy neoactivity phenotype, e.g., 2HG, e.g., R-2HG, phenotype.
`Evaluating the alpha hydroxyl, e.g., 2HG, genotype can comprise determining if an
`IDHl or IDH2 mutation having alpha hydroxy neoactivity, e.g., 2HG neoactivity, is
`present, e.g., a mutation disclosed herein having alpha hydroxy neoactivity, e.g., 2HG
`neoactivity. Alpha hydroxy neoactivity phenotype, e.g., 2HG, e.g., R-2HG,
`phenotype, as used herein, refers to the level of alpha hydroxy neoactivity product,
`e.g., 2HG, e.g., R-2HG, level of alpha hydroxy neoactivity, e.g., 2HG neoactivity, or
`level of mutant enzyme having alpha hydroxy neoactivity, e.g., 2HG neoactivity (or
`corresponding mRNA). The evaluation can be by a method described herein.
`In an embodiment the subject can be evaluated, before or after treatment, to
`determine if the cell proliferation-related disorder is characterized by an alpha
`hydroxy neoactivity product, e.g., 2HG, e.g., R-2HG.
`In an embodiment a cancer, e.g., a glioma or brain tumor in a subject, can be
`analyzed, e.g., by imaging and/or spectroscopic analysis, e.g., magnetic resonance(cid:173)
`based analysis, e.g., MRI and/or MRS, e.g., before or after treatment, to determine if
`it is characterized by presence of an alpha hydroxy neoactivity product, e.g., 2HG,
`e.g., R-2HG.
`
`In an embodiment the method comprises evaluating, e.g., by direct
`examination or evaluation of the subject, or a sample from the subject, or receiving
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`such information about the subject, the IDH, e.g., IDBI or IDH2, genotype, or an
`alpha hydroxy neoactivity product, e.g., 2HG, e.g., R-2HG phenotype of, the subject,
`e.g., of a cell, e.g., a cancer cell, characterized by the cell proliferation-related
`disorder. (As described in more detail elsewhere herein the evaluation can be, e.g., by
`DNA sequencing, immuno analysis, evaluation of the presence, distribution or level
`of an alpha hydroxy neoactivity product, e.g., 2HG, e.g., R-2HG, e.g., from
`spectroscopic analysis, e.g., magnetic resonance-based analysis, e.g., MRI and/or
`MRS measurement, sample analysis such as serum or spinal cord fluid analysis, or by
`analysis of surgical material, e.g., by mass-spectroscopy). In embodiments this
`information is used to determine or confirm that a proliferation-related disorder, e.g.,
`a cancer, is characterized by an alpha hydroxy neoactivity product, e.g., 2HG, e.g., R-
`2HG. In embodiments this information is used to determine or confirm that a cell
`proliferation-related disorder, e.g., a cancer, is characterized by an IDH, e.g., IDBI or
`IDH2, allele described herein, e.g., an IDBI allele having a mutation, e.g., a His, Ser,
`Cys, Gly, Val, Pro or Leu (e.g., His, Ser, Cys, Gly, Val, or Leu at residue 132, more
`specifically, His or Cys, or an IDH2 allele having a mutation at residue 172, e.g., a K,
`M, S,G, orW.
`
`In an embodiment, before and/or after treatment has begun, the subject is
`evaluated or monitored by a method described herein, e.g., the analysis of the
`presence, distribution, or level of an alpha hydroxy neoactivity product, e.g., 2HG,
`e.g., R-2HG, e.g., to select, diagnose or prognose the subject, to select an inhibitor, or
`to evaluate response to the treatment or progression of disease.
`In an embodiment the cell proliferation-related disorder is a tumor of the CNS,
`e.g., a glioma, a leukemia, e.g., AML or ALL, e.g., B-ALL or T-ALL, prostate cancer,
`fibrosarcoma, paraganglioma, or myelodysplasia or myelodysplastic syndrome ( e.g.,
`B-ALL or T-ALL, prostate cancer, or myelodysplasia or myelodysplastic syndrome)
`and the evaluation is: evaluation of the presence, distribution, or level of an alpha
`hydroxy neoactivity product, e.g., 2HG, e.g., R-2HG; or evaluation of the presence,
`distribution, or level of a neoactivity, e.g., an alpha hydroxy neoactivity, e.g., 2HG
`neoactivity, of an IDBI or IDH2, mutant protein.
`In an embodiment the disorder is other than a solid tumor. In an embodiment
`the disorder is a tumor that, at the time of diagnosis or treatment, does not have a
`necrotic portion. In an embodiment the disorder is a tumor in which at least 30, 40,
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`50, 60, 70, 80 or 90% of the tumor cells carry an IHD, e.g., IDHl or IDH2, mutation
`having 2HG neoactivity, at the time of diagnosis or treatment.
`In an embodiment the cell proliferation-related disorder is a cancer, e.g., a
`cancer described herein, characterized by an IDHl somatic mutant having alpha
`hydroxy neoactivity, e.g., 2HG neoactivity, e.g., a mutant described herein. In an
`embodiment the tumor is characterized by increased levels of an alpha hydroxy
`neoactivity product, 2HG, e.g., R-2HG, as compared to non-diseased cells of the same
`type.
`
`In an embodiment the method comprises selecting a subject having a glioma,
`on the basis of the cancer being characterized by unwanted (i.e., increased) levels of
`an alpha hydroxy neoactivity, product, e.g., 2HG, e.g., R-2HG.
`In an embodiment the cell proliferation-related disorder is a tumor of the CNS,
`e.g., a glioma, e.g., wherein the tumor is characterized by an IDHl somatic mutant
`having alpha hydroxy neoactivity, e.g., 2HG neoactivity, e.g., a mutant described
`herein. Gliomas include astrocytic tumors, oligodendroglial tumors, oligoastrocytic
`tumors, anaplastic astrocytomas, and glioblastomas. In an embodiment the tumor is
`characterized by increased levels of an alpha hydroxy neoactivity product, e.g., 2HG,
`e.g., R-2HG, as compared to non-diseased cells of the same type. E.g., in an
`embodiment, the IDHl allele encodes an IDHl having other than an Arg at residue
`132. E.g., the allele encodes His, Ser, Cys, Gly, Val, Pro or Leu (e.g., His, Ser, Cys,
`Gly, Val, or Leu), or any residue described in Yan et al., at residue 132, according to
`the sequence of SEQ ID NO:8 (see also Fig. 21). In an embodiment the allele
`encodes an IDHl having His at residue 132. In an embodiment the allele encodes an
`IDHl having Ser at residue 132.
`In an embodiment the IDHl allele has an A (or any other nucleotide other than
`C) at nucleotide position 394, or an A (or any other nucleotide other than G) at
`nucleotide position 395. In an embodiment the allele is a C394A, a C394G, a C394T,
`a G395C, a G395T or a G395A mutation; specifically a C394A or a G395A mutation
`according to the sequence of SEQ ID NO:5.
`In an embodiment the method comprises selecting a subject having a glioma,
`wherein the cancer is characterized by having an IDHl allele described herein, e.g.,
`an IDHl allele having His, Ser, Cys, Gly, Val, Pro or Leu at residue 132 (SEQ ID
`NO:8), more specifically His, Ser, Cys, Gly, Val, or Leu; or His or Cys.
`
`- 9 -
`
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`

`WO 2010/105243
`
`PCT/0S2010/027253
`
`In an embodiment the method comprises selecting a subject having a glioma,
`on the basis of the cancer being characterized by an IDHl allele described herein, e.g.,
`an IDHl allele having His, Ser, Cys, Gly, Val, Pro or Leu at residue 132 (SEQ ID
`NO:8), more specifically His, Ser, Cys, Gly, Val, or Leu; or His or Cys.
`In an embodiment the method comprises selecting a subject having a glioma,
`on the basis of the cancer being characterized by increased levels of an alpha hydroxy
`neoactivity, product, e.g., 2HG, e.g., R-2HG.
`In an embodiment the method comprises selecting a subject having a
`fibrosarcoma or paraganglioma wherein the cancer is characterized by having an
`IDHl allele described herein, e.g., an IDHl allele having Cys at residue 132 (SEQ ID
`NO:8).
`
`In an embodiment the method comprises selecting a subject having a
`fibrosarcoma or paraganglioma, on the basis of the cancer being characterized by an
`IDHl allele described herein, e.g., an IDHl allele having Cys at residue 132 (SEQ ID
`NO:8).
`
`In an embodiment the method comprises selecting a subject having a
`fibrosarcoma or paraganglioma, on the basis of the cancer being characterized by
`increased levels of an alpha hydroxy neoactivity, product, e.g., 2HG, e.g., R-2HG.
`In an embodiment the cell proliferation-related disorder is localized or
`metastatic prostate cancer, e.g., prostate adenocarcinoma, e.g., wherein the cancer is
`characterized by an IDHl somatic mutant having alpha hydroxy neoactivity, e.g.,
`2HG neoactivity, e.g., a mutant described herein. In an embodiment the cancer is
`characterized by increased levels of an alpha hydroxy neoactivity product, e.g., 2HG,
`e.g., R-2HG, as compared to non-diseased cells of the same type.
`E.g., in an embodiment, the IDHl allele encodes an IDHl having other than
`an Arg at residue 132. E.g., the allele encodes His, Ser, Cys, Gly, Val, Pro or Leu, or
`any residue described in Kang et al, 2009, Int. J. Cancer, 125: 353-355 at residue 132,
`according to the sequence of SEQ ID NO:8 (see also FIG. 21) ( e.g., His, Ser, Cys,
`Gly, Val, or Leu). In an embodiment the allele encodes an IDHl having His or Cys at
`residue 132.
`In an embodiment the IDHI allele has a T (or any other nucleotide other than
`C) at nucleotide position 394, or an A (or any other nucleotide other than G) at
`nucleotide position 395. In an embodiment the allele is a C394T or a G395A
`mutation according to the sequence of SEQ ID NO:5.
`
`Rigel Exhibit 1009
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`WO 2010/105243
`
`PCT/0S2010/027253
`
`In an embodiment the method comprises selecting a subject having prostate
`cancer, e.g., prostate adenocarcinoma, wherein the cancer is characterized by an IDHl
`allele described herein, e.g., an IDHl allele having His or Cys at residue 132 (SEQ ID
`N0:8).
`
`In an embodiment the method comprises selecting a subject having prostate
`cancer, e.g., prostate adenocarcinoma, on the basis of the cancer being characterized
`by an IDHl allele described herein, e.g., an IDHl allele having His or Cys at residue
`132 (SEQ ID N0:8).
`In an embodiment the method comprises selecting a subject having prostate
`cancer, on the basis of the cancer being characterized by increased levels of an alpha
`hydroxy neoactivity product, e.g., 2HG, e.g., R-2HG.
`In an embodiment the cell proliferation-related disorder is a hematological
`cancer, e.g., a leukemia, e.g., AML, or ALL, wherein the hematological cancer is
`characterized by an IDHl somatic mutant having alpha hydroxy neoactivity, e.g.,
`2HG neoactivity, e.g., a mutant described herein. In an embodiment the cancer is
`characterized by increased levels of an alpha hydroxy neoactivity product, e.g., 2HG,
`e.g., R-2HG, as compared to non-diseased cells of the same type.
`In an embodiment the cell proliferation-related disorder is acute lymphoblastic
`leukemia (e.g., an adult or pediatric form), e.g., wherein the acute lymphoblastic
`leukemia (sometimes referred to herein as ALL) is characterized by an IDHl somatic
`mutant having alpha hydroxy neoactivity, e.g., 2HG neoactivity, e.g., a mutant
`described herein. The ALL can be, e.g., B-ALL or T-ALL. In an embodiment the
`cancer is characterized by increased levels of 2 an alpha hydroxy neoactivity product,
`e.g., HG, e.g., R-2HG, as compared to non-diseased cells of the same type. E.g., in an
`embodiment, the IDHl allele is an IDHl having other than an Arg at residue 132
`(SEQ ID N0:8). E.g., the allele encodes His, Ser, Cys, Gly, Val, Pro or Leu, or any
`residue described in Kang et a.l, at residue 132, according to the sequence of SEQ ID
`N0:8 (see also FIG. 21), more specifically His, Ser, Cys, Gly, Val, or Leu. In an
`embodiment the allele encodes an IDHl having Cys at residue 132.
`In an embodiment the IDHl allele has a T (or any other nucleotide other than
`C) at nucleotide position 394. In an embodiment the allele is a C394T mutation
`according to the sequence of SEQ ID N0:5.
`
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`Page 12 of 245
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`WO 2010/105243
`
`PCT/0S2010/027253
`
`In an embodiment the method comprises selecting a subject having ALL, e.g.,
`B-ALL or T-ALL, characterized by an IDHl allele described herein, e.g., an IDHl
`allele having Cys at residue 132 according to the sequence of SEQ ID N0:8.
`In an embodiment the method comprises selecting a subject ALL, e.g., B-ALL
`or T-ALL, on the basis of cancer being characterized by having an IDHl allele
`described herein, e.g., an IDHl allele having Cys at residue 132 (SEQ ID N0:8).
`In an embodiment the method comprises selecting a subject having ALL, e.g.,
`B-ALL or T-ALL, on the basis of the cancer being characterized by increased levels
`of an alpha hydroxy neoactivity product, e.g., 2HG, e.g., R-2HG.
`In an embodiment the cell proliferation-related disord